CliqueTrees

Author: samuelsonric

Project.toml

@@ -7,37 +7,14 @@ version = "0.2.0"
 AMD = "14f7f29c-3bd6-536c-9a0b-7339e30b5a3e"
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
-DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+CliqueTrees = "60701a23-6482-424a-84db-faee86b9b1f8"
 MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
 PartialFunctions = "570af359-4316-4cb7-8c74-252c00c2016b"
-Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
-SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
-Sparspak = "e56a9233-b9d6-4f03-8d0f-1825330902ac"
-
-[weakdeps]
-Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
-Laplacians = "6f8e5838-0efe-5de0-80a3-5fb4f8dbb1de"
-Metis = "2679e427-3c69-5b7f-982b-ece356f1e94b"
-TreeWidthSolver = "7d267fc5-9ace-409f-a54c-cd2374872a55"
-
-[extensions]
-GraphsExt = "Graphs"
-LaplaciansExt = "Laplacians"
-MetisExt = "Metis"
-TreeWidthSolverExt = "TreeWidthSolver"
 
 [compat]
-AMD = "0.5"
 AbstractTrees = "0.4"
 Catlab = "0.16"
-DataStructures = "0.18"
-Graphs = "1.12"
-Laplacians = "1.1"
+CliqueTrees = "0.5.1"
 MLStyle = "0.4"
-Metis = "1"
 PartialFunctions = "1.1"
-Reexport = "1.2.2"
-Sparspak = "0.3"
-TreeWidthSolver = "0.3"
 julia = "1.10"

ext/GraphsExt.jl

@@ -1,16 +1,9 @@
 module StructuredDecompositions
 
 
-using Reexport
-
-
-include("junction_trees/JunctionTrees.jl")
 include("decompositions/Decompositions.jl")
 include("functor_utils/FunctorUtils.jl")
 include("deciding_sheaves/DecidingSheaves.jl")
 
 
-@reexport using .JunctionTrees
-
-
 end 

ext/LaplaciansExt.jl

@@ -5,26 +5,23 @@ export StructuredDecomposition, StrDecomp,
       𝐃, bags, adhesions, adhesionSpans, 
       ∫
 
-using ..JunctionTrees
-using ..JunctionTrees: PermutationOrAlgorithm, EliminationAlgorithm, SupernodeType, DEFAULT_ELIMINATION_ALGORITHM, DEFAULT_SUPERNODE_TYPE
+using AbstractTrees
+using CliqueTrees
+using CliqueTrees: PermutationOrAlgorithm, EliminationAlgorithm, SupernodeType, DEFAULT_ELIMINATION_ALGORITHM, DEFAULT_SUPERNODE_TYPE
 
 using PartialFunctions
 using MLStyle
 
-using Base: DEFAULT_STABLE, ForwardOrdering
-using Base.Threads
 using Catlab
 using Catlab.CategoricalAlgebra
 using Catlab.Graphs
 using Catlab.Graphs: add_edges!
 using Catlab.ACSetInterface
 using Catlab.CategoricalAlgebra.Diagrams
-using SparseArrays: getcolptr
-using SparseArrays
 
 import Catlab.CategoricalAlgebra.Diagrams: ob_map, hom_map, colimit, limit
 
 include("str_decomps.jl")
-include("junction_trees.jl")
+include("clique_trees.jl")
 
 end

ext/MetisExt.jl

@@ -3,26 +3,30 @@
         alg::PermutationOrAlgorithm=DEFAULT_ELIMINATION_ALGORITHM,
         snd::SupernodeType=DEFAULT_SUPERNODE_TYPE)
 
-Construct a structured decomposition of a simple graph. See [`junctiontree`](@ref) for the meaning of `alg` and `snd`.
+Construct a structured decomposition of a simple graph. See [`cliquetree`](@ref) for the meaning of `alg` and `snd`.
 """
 function StrDecomp(graph::HasGraph; alg::PermutationOrAlgorithm=DEFAULT_ELIMINATION_ALGORITHM, snd::SupernodeType=DEFAULT_SUPERNODE_TYPE)
-    label, tree = junctiontree(adjacency_matrix(graph); alg, snd)
-    relative!(tree)
+    label, tree = cliquetree(symmetrize(graph); alg, snd)
     n = length(tree)
     shape = Graph(n)
 
-    for i in 1:n - 1
-        add_edge!(shape, parentindex(tree, i), i)
+    for i in 1:n
+        j = parentindex(tree, i)
+        
+        if !isnothing(j)
+            add_edge!(shape, j, i)
+        end
     end
 
     diagram = FinDomFunctor(homomorphisms(graph, label, tree)..., ∫(shape))
     StrDecomp(shape, diagram, Decomposition, dom(diagram))
 end
 
 
-function homomorphisms(graph::HasGraph, label::AbstractVector, tree::JunctionTree)
+function homomorphisms(graph::HasGraph, label::AbstractVector, tree::CliqueTree)
     m = length(collect(rootindices(tree)))
     n = length(tree)
+    relative = relatives(tree)
     subgraph = Vector{Any}(undef, 2n - m)
     homomorphism = Vector{Any}(undef, 2n - 2m)
 
@@ -43,7 +47,7 @@ function homomorphisms(graph::HasGraph, label::AbstractVector, tree::JunctionTre
             subgraph[n + k] = induced_subgraph(graph, view(label, separator(tree, i)))
 
             # separator(i) → bag(j)
-            homomorphism[k] = induced_homomorphism(subgraph[n + k], subgraph[j], relative(tree, i))
+            homomorphism[k] = induced_homomorphism(subgraph[n + k], subgraph[j], CliqueTrees.neighbors(relative, i))
 
             # separator(i) → bag(i)
             homomorphism[n - m + k] = induced_homomorphism(subgraph[n + k], subgraph[i], length(residual(tree, i)) .+ eachindex(separator(tree, i)))
@@ -72,24 +76,13 @@ function induced_homomorphism(domain::HasGraph, codomain::HasGraph, V::AbstractV
 end
 
 
-# Construct the adjacency matrix of an undirected graph.
-function adjacency_matrix(graph::HasGraph)
-    symmetric = SymmetricGraph(nv(graph))
-    add_edges!(symmetric, src(graph), tgt(graph))
-    adjacency_matrix(symmetric)
+function symmetrize(graph::AbstractSymmetricGraph)
+    graph
 end
 
 
-function adjacency_matrix(graph::AbstractSymmetricGraph)
-    matrix = spzeros(Bool, Int, nv(graph), nv(graph))
-    sizehint!(rowvals(matrix), ne(graph))
-
-    for v in vertices(graph)
-        append!(rowvals(matrix), neighbors(graph, v))
-        getcolptr(matrix)[v + 1] = length(rowvals(matrix)) + 1
-    end
-
-    resize!(nonzeros(matrix), ne(graph))
-    fill!(nonzeros(matrix), true)
-    matrix
+function symmetrize(graph::HasGraph)
+    symmetric = SymmetricGraph(nv(graph))
+    add_edges!(symmetric, src(graph), tgt(graph))
+    symmetric
 end